If you are pulling from git, you need to run ./autogen.sh before ./configure.
[minepeon@minion bfgminer]$ ./autogen.sh
Getting submodules...
Running autoreconf -if...
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.'.
libtoolize: copying file `./ltmain.sh'
libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.ac and
libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
Makefile.am:40: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
Updating version.h...
cmp: version.h: No such file or directory
It is still pointing to version.h